You could also check out PlayOnLinux which uses a modified version of Wine, which is optimized for certain games through user-patches and more. Try to post the error messages on WineHQ, or in the IRC-channel #winehq on. The good news is that according to the appdb of WineHQ, Quake II should be runable on Ubuntu.
Try to invoke the verbose option if it exists and 'wine quakeii.exe' doesn't yield any results, e.g. Top English News Headline - Find latest breaking news from India and world about politics, entertainment, movie review, Sports, business and more at Jagran. If you run man wine you will probably find a verbose option (maybe -v?). Try to run your game with your terminal environment through wine with 'wine quakeii.exe' or equivalent. In regards to your question I can't really give you any guidance, without error messages and/or other terminal outputs. Happy exploring and don't be afraid to play around with Ubuntu :-) I'm pretty certain I speak for a vast majority of linux users when I say that if you can find the joy of exploring how thing works within linux, fixing stuff wont seem like such a chore anymore. Great to hear that you feel you're getting comfortable using the terminal and Ubuntu.
